Contacts of the helix formed by residues 45 - 60 (chain C) in PDB entry 1C17
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 45 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C PRO* 3.2 10.9 - - + -
44C ASP* 1.3 79.5 - - - +
46C ILE* 1.3 86.2 + - + +
48C LEU* 4.1 1.6 - - - +
49C LEU* 3.7 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C PRO* 5.5 6.7 - - + -
45C LEU* 1.3 99.2 - - + +
47C PRO* 1.3 77.4 - - + +
49C LEU* 3.1 22.9 + - + +
50C ARG* 3.1 14.9 + - + +
44D ASP* 4.3 23.8 - - + +
48D LEU* 6.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C PHE* 3.6 3.0 - - + -
36C LEU* 6.5 0.4 - - + -
39C ALA* 3.7 39.3 - - + +
42C GLN* 4.5 11.9 - - + +
43C PRO* 2.6 29.4 - - + +
44C ASP* 4.3 1.8 - - - -
46C ILE* 1.3 98.5 - - + +
48C LEU* 1.3 54.9 + - - +
50C ARG* 4.3 7.9 - - + -
51C THR* 2.4 47.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ILE* 6.2 1.3 - - + -
50B ARG* 4.4 26.5 + - + +
44C ASP* 2.7 47.5 - - + +
45C LEU 4.1 2.9 - - - +
46C ILE 3.2 0.8 - - - -
47C PRO* 1.3 80.1 - - - +
49C LEU* 1.3 62.9 + - - +
51C THR* 3.8 7.1 - - - -
52C GLN* 3.2 33.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LEU 3.7 11.1 + - - +
46C ILE* 3.1 15.8 + - + +
48C LEU* 1.3 79.3 - - + +
50C ARG* 1.3 64.6 + - + +
52C GLN* 2.7 40.6 - - + +
53C PHE* 3.3 10.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C PHE* 3.3 19.1 - - + -
46C ILE* 3.1 14.9 + - + +
47C PRO* 3.8 4.7 - - + +
49C LEU* 1.3 78.2 - - + +
51C THR* 1.3 65.5 + - - +
53C PHE* 3.1 36.1 + - - +
54C PHE* 3.0 46.9 + - - -
48D LEU* 4.4 25.8 + - + +
51D THR* 4.0 13.7 - - - +
52D GLN* 4.3 12.3 - - - +
55D ILE* 3.2 27.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PHE* 5.9 0.9 - - + -
50B ARG* 3.9 17.9 - - - +
54B PHE* 4.3 15.9 - - + -
32C GLY* 4.9 7.0 - - - +
35C PHE* 3.0 28.4 - - + -
36C LEU* 5.1 16.1 - - + +
47C PRO* 2.4 32.9 + - - +
48C LEU* 3.8 7.6 - - - -
50C ARG* 1.3 73.2 - - - +
52C GLN* 1.3 62.6 + - - +
54C PHE* 3.1 4.7 + - - +
55C ILE* 3.0 26.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ARG* 4.2 8.1 - - - +
53B PHE* 6.4 2.0 - - + -
48C LEU* 3.2 21.4 + - + +
49C LEU* 2.7 47.2 - - + +
51C THR* 1.3 75.1 - - - +
53C PHE* 1.3 61.2 + - - +
55C ILE* 3.4 13.0 - - + -
56C VAL* 2.7 52.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LEU* 3.7 12.6 - - + +
50C ARG* 3.1 44.0 - - - +
52C GLN* 1.3 84.2 - - + +
54C PHE* 1.3 56.9 + + - +
56C VAL* 4.2 4.2 - - + +
57C MET* 2.9 51.3 + - + +
52D GLN* 6.5 0.9 - - + -
55D ILE* 5.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ILE* 5.3 0.3 - - - -
31C LEU* 3.0 50.3 - - + +
35C PHE* 3.3 39.0 - + + -
50C ARG* 3.0 44.6 + - - -
51C THR* 3.1 6.8 + - - +
52C GLN 3.0 1.2 + - - -
53C PHE* 1.3 73.8 - - - +
55C ILE* 1.3 61.0 + - + +
56C VAL 2.9 1.3 - - - -
57C MET* 2.6 33.4 + - + +
58C GLY* 2.9 9.5 + - - -
32D GLY 5.2 2.5 - - - -
51D THR* 4.3 7.2 - - + -
55D ILE* 3.2 49.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ARG* 3.2 32.5 - - - +
53B PHE* 5.4 3.1 - - + -
54B PHE* 3.2 33.2 - - + -
57B MET* 4.4 14.6 - - + -
28C ILE* 3.2 34.2 - - + +
32C GLY* 3.4 27.5 - - - -
51C THR* 3.0 10.9 + - + +
52C GLN* 3.2 17.3 - - + +
54C PHE* 1.3 76.4 - - - +
56C VAL* 1.3 63.7 + - + +
59C LEU* 2.9 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PHE* 6.4 1.1 - - + -
57B MET* 5.7 3.4 - - + -
52C GLN* 2.7 46.3 + - + +
53C PHE* 4.2 3.8 - - + +
54C PHE 2.8 0.2 + - - -
55C ILE* 1.3 78.0 - - + +
57C MET* 1.3 51.2 + - - +
58C GLY 2.8 4.0 - - - -
59C LEU* 2.6 36.4 + - + -
60C VAL* 2.7 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 5.0 1.3 - - + -
53C PHE* 2.9 59.6 + - + +
54C PHE* 2.6 22.6 + - + +
56C VAL* 1.3 72.1 - - - +
58C GLY* 1.3 57.4 + - - +
60C VAL* 3.6 8.1 + - - +
61C ASP* 3.4 18.0 + - - +
28D ILE* 4.2 26.9 - - + -
55D ILE* 4.5 20.2 - - + +
56D VAL* 5.7 3.4 - - + -
59D LEU* 4.1 40.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ALA* 3.0 34.6 - - - +
27C GLY* 5.2 1.8 - - - -
28C ILE* 3.0 25.1 - - - +
31C LEU* 6.1 0.8 - - - +
54C PHE 2.9 9.5 + - - -
56C VAL 2.8 1.0 - - - -
57C MET* 1.3 77.4 - - - +
59C LEU* 1.3 55.2 + - - +
60C VAL 3.0 4.9 - - - -
61C ASP* 3.1 11.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B MET* 4.0 37.0 - - + +
61B ASP* 5.4 7.9 - - + +
24C ALA* 5.3 0.2 - - - -
28C ILE* 2.9 14.1 - - + +
55C ILE 2.9 15.1 + - - +
56C VAL* 2.6 26.8 + - + +
58C GLY* 1.3 71.5 - - - +
60C VAL* 1.3 58.3 + - + +
61C ASP 3.5 0.4 - - - -
62C ALA* 4.6 5.2 + - + +
63C ILE* 3.7 19.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C VAL* 2.7 35.2 + - + +
57C MET* 3.9 9.2 - - - +
58C GLY 3.0 0.2 - - - -
59C LEU* 1.3 82.0 - - + +
61C ASP* 1.3 50.6 + - - +
62C ALA 3.3 2.5 - - - -
63C ILE* 4.0 16.2 - - + -
64C PRO* 2.7 36.3 - - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il